tractography

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tractography

Gonzalo Rojas Costa
Hi:

  I wanto to get the corticospinal tract... I draw two ROIs: one in
the right hemisphere midbrain, and the other in the primary motor area
of the same hemisphere... I draw both ROIs with the same label
value... But, I got tracts that pass through the first ROI or the
second ROI, and both ROIs simultaneously... I only want the tracts
that pass only through both ROIs simultaneously.. How can I get it
?...

  I used 3D Slicer 4.5.0-1 r24735 in Ubuntu...

  Sincerely,


Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of Radiology
Clínica las Condes
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-97771785
www.clc.cl
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Re: tractography

O'Donnell, Lauren J., Ph.D.
Dear Gonzalo,

To get tracts that pass through both, you will need to use two different label values, one for each ROI.  You can use the change island function in the editor to change the label for one ROI.

Then in Diffusion->Tractography->Fiber Bundle Label Select you can use the AND operation to get fibers that pass through both of the two different labels. You list the labels like this: 1, 2 (with a comma separating the label values).

I hope this helps. 

Best regards,
Lauren

Lauren J. O’Donnell, Ph.D.
Assistant Professor, Harvard Medical School
http://scholar.harvard.edu/laurenjodonnell
1249 Boylston St., Room #210
Boston, Massachusetts 02215
[hidden email]


On May 25, 2016, at 12:05 PM, Gonzalo Rojas Costa <[hidden email]> wrote:

Hi:

 I wanto to get the corticospinal tract... I draw two ROIs: one in
the right hemisphere midbrain, and the other in the primary motor area
of the same hemisphere... I draw both ROIs with the same label
value... But, I got tracts that pass through the first ROI or the
second ROI, and both ROIs simultaneously... I only want the tracts
that pass only through both ROIs simultaneously.. How can I get it
?...

 I used 3D Slicer 4.5.0-1 r24735 in Ubuntu...

 Sincerely,


Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of Radiology
Clínica las Condes
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-97771785
www.clc.cl
_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ


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Re: tractography

Gonzalo Rojas Costa
In reply to this post by Gonzalo Rojas Costa

Hi Lauren:

What it means the "Input Fiber Bundle" in Diffusion->Tractography->Fiber Bundle Label Select ?

Sincerely,

Gonzalo Rojas Costa

------------------------------------
Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of Radiology
Clinica las Condes
Lo Fontecilla 441, Las Condes, Santiago, Chile
Tel: 56-2-2105170
Cel: 56-9-97771785
www.clc.cl

El 25/5/2016 13:02, "O'Donnell, Lauren J., Ph.D." <[hidden email]> escribió:
Dear Gonzalo,

To get tracts that pass through both, you will need to use two different label values, one for each ROI.  You can use the change island function in the editor to change the label for one ROI.

Then in Diffusion->Tractography->Fiber Bundle Label Select you can use the AND operation to get fibers that pass through both of the two different labels. You list the labels like this: 1, 2 (with a comma separating the label values).

I hope this helps. 

Best regards,
Lauren

Lauren J. O’Donnell, Ph.D.
Assistant Professor, Harvard Medical School
http://scholar.harvard.edu/laurenjodonnell
1249 Boylston St., Room #210
Boston, Massachusetts 02215
[hidden email]


On May 25, 2016, at 12:05 PM, Gonzalo Rojas Costa <[hidden email]> wrote:

Hi:

 I wanto to get the corticospinal tract... I draw two ROIs: one in
the right hemisphere midbrain, and the other in the primary motor area
of the same hemisphere... I draw both ROIs with the same label
value... But, I got tracts that pass through the first ROI or the
second ROI, and both ROIs simultaneously... I only want the tracts
that pass only through both ROIs simultaneously.. How can I get it
?...

 I used 3D Slicer 4.5.0-1 r24735 in Ubuntu...

 Sincerely,


Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of Radiology
Clínica las Condes
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: <a href="tel:56-9-97771785" value="&#43;56997771785" target="_blank">56-9-97771785
www.clc.cl
_______________________________________________
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.


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Re: tractography

inorton
On Wed, May 25, 2016 at 1:44 PM, Gonzalo Rojas Costa <[hidden email]> wrote:

What it means the "Input Fiber Bundle" in Diffusion->Tractography->Fiber Bundle Label Select ?

There is a module called "FiberBundleLabelSelect":


After seeding, you can use this module to select fiberbundles passing through two different labelmap colors (you would need to change the color of one of the ROIs, using the editor "Change Island" effect).

The other option is to use the TractographyDisplay module to do sub-selection using ROI boxes:


Best,
Isaiah
 

Sincerely,

Gonzalo Rojas Costa

------------------------------------
Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of Radiology
Clinica las Condes
Lo Fontecilla 441, Las Condes, Santiago, Chile
Tel: 56-2-2105170
Cel: 56-9-97771785
www.clc.cl

El 25/5/2016 13:02, "O'Donnell, Lauren J., Ph.D." <[hidden email]> escribió:
Dear Gonzalo,

To get tracts that pass through both, you will need to use two different label values, one for each ROI.  You can use the change island function in the editor to change the label for one ROI.

Then in Diffusion->Tractography->Fiber Bundle Label Select you can use the AND operation to get fibers that pass through both of the two different labels. You list the labels like this: 1, 2 (with a comma separating the label values).

I hope this helps. 

Best regards,
Lauren

Lauren J. O’Donnell, Ph.D.
Assistant Professor, Harvard Medical School
http://scholar.harvard.edu/laurenjodonnell
1249 Boylston St., Room #210
Boston, Massachusetts 02215
[hidden email]


On May 25, 2016, at 12:05 PM, Gonzalo Rojas Costa <[hidden email]> wrote:

Hi:

 I wanto to get the corticospinal tract... I draw two ROIs: one in
the right hemisphere midbrain, and the other in the primary motor area
of the same hemisphere... I draw both ROIs with the same label
value... But, I got tracts that pass through the first ROI or the
second ROI, and both ROIs simultaneously... I only want the tracts
that pass only through both ROIs simultaneously.. How can I get it
?...

 I used 3D Slicer 4.5.0-1 r24735 in Ubuntu...

 Sincerely,


Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of Radiology
Clínica las Condes
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: <a href="tel:56-9-97771785" value="&#43;56997771785" target="_blank">56-9-97771785
www.clc.cl
_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.


_______________________________________________
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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ


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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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